In the local VA district, who determines which VHA directives they follow and which one the district gets to ignore?

No one on RallyPoint can provide an answer. Have you talked to the folks at the local VA district about your issue?

They ate all supposed to be followed as they are not optional.

VA wide policies should be adhered to regardless of geographic location. Specific hospitals may have additional policies that manage the care they provide and their branch locations/clinics but it would generally be for that specific Hospital. For example some Hospitals are considered branch locations of larger Hospitals. Truman VA Hospital in Columbia Missouri is a branch off of the much larger Kansas City Hospital.